I used to be able to connect the Flux Point and Flux Plug to EU machines, but I am no longer able to. Since I have used this to transfer between EU and RF, and all my power starts out as RF, my entire EU-based infrastructure now must be completely redone.

If it was a bug in previous versions that allowed this to be accomplished but has now been fixed, I would love it if there was a config option added that decides whether this functionality is possible or not. If it wasn't a bug in previous versions, but was actually a feature that a new bug is now preventing, I would love it if was fixed.

IC2 should still work supposedly, i'll look into it

Fixed in dev. You'll need to update Sonar Core (when the update is out)